Cytochrome P450 2C9 type II binding studies on quinoline-4-carboxamide analogues

Journal of Medicinal Chemistry

Volumn 51, Issue 24, 2008, Pages 8000-8011

  Peng, Chi Chi ^a   Cape, Jonathan L ^c   Rushmore, Tom ^b   Crouch, Gregory J ^a   Jones, Jeffrey P ^a  

^a WASHINGTON STATE UNIVERSITY   (United States)

^b MERCK RESEARCH LABORATORIES   (United States)

^c NONE

Author keywords

[No Author keywords available]

Indexed keywords

AMIDE; ARGININE; CYTOCHROME P450 2C9; DICLOFENAC; HEME; NAPHTHALENE DERIVATIVE; NITROGEN; PYRIDINE; QUINOLINE 4 CARBOXAMIDE DERIVATIVE; QUINOLINE DERIVATIVE; UNCLASSIFIED DRUG;

ARTICLE; BINDING AFFINITY; DISSOCIATION CONSTANT; DRUG BINDING; DRUG DESIGN; DRUG METABOLISM; DRUG SYNTHESIS; ELECTRICITY; ENZYME ACTIVE SITE; HYDROPHOBICITY; ISOMER; MOLECULAR INTERACTION; NONHUMAN; SOLVATION; STEREOCHEMISTRY; STRUCTURE ACTIVITY RELATION; ULTRAVIOLET SPECTROSCOPY;

ARGININE; ARYL HYDROCARBON HYDROXYLASES; CATALYTIC DOMAIN; CHEMISTRY, PHARMACEUTICAL; DRUG DESIGN; HEME; HUMANS; IMIDAZOLES; IRON; MODELS, MOLECULAR; MOLECULAR CONFORMATION; PROTEIN BINDING; QUINOLINES; STRUCTURE-ACTIVITY RELATIONSHIP; SUBSTRATE SPECIFICITY;

EID: 58149099402     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm8011257     Document Type: Article

References (47)

1. Locuson, C. W.; Wahlstrom, J. L.; Rock, D. A.; Rock, D. A.; Jones, J. P. A new class of CYP2C9 inhibitors: Probing 2C9 specificity with high-affinity benzbromarone derivatives. Drug Metab. Dispos. 2003, 31, 967-971.
2. Locuson, C. W.; Suzuki, H.; Rettie, A. E.; Jones, J. P. Charge and substituent effects on affinity and metabolism of benzbromarone-based CYP2C19 inhibitors. J. Med. Chem. 2004, 47, 6768-6776.
3. Locuson, C. W.; Rock, D. A.; Jones, J. P. Quantitative binding models for CYP2C9 based on benzbromarone analogues. Biochemistry 2004, 43, 6948-6958.
4. Rettie, A. E.; Jones, J. P. Clinical and toxicological relevance of CYP2C9: Drug-drug interactions and pharmacogenetics. Annu. Rev. Pharmacol. Toxicol. 2005, 45, 477-494.
5. Hudelson, M. G.; Jones, J. P. Line-walking method for predicting the inhibition of P450 drug metabolism. J. Med. Chem. 2006, 49, 4367-4373.
6. Hudelson, M. G.; Ketkar, N. S.; Holder, L. B.; Carlson, T. J.; Peng, C. C.; Waldher, B. J.; Jones, J. P. High confidence predictions of drug-drug interactions: predicting affinities for cytochrome P450 2C9 with multiple computational methods. J. Med. Chem. 2008, 51, 648-654.
7. Schenkman, J. B. Studies on the nature of the type I and type II spectral changes in liver microsomes. Biochemistry 1970, 9, 2081-2091.
8. Kumaki, K.; Sato, M.; Kon, H.; Nebert, D. W. Correlation of type I, type II, and reverse type I difference spectra with absolute changes in spin state of hepatic microsomal cytochrome P-450 iron from five mammalian species. J. Biol. Chem. 1978, 253, 1048-1058.
9. Schenkman, J. B.; Remmer, H.; Estabrook, R. W. Spectral studies of drug interaction with hepatic microsomal cytochrome. Mol. Pharmacol. 1967, 3, 113-123.
10. Locuson, C. W.; Hutzler, J. M.; Tracy, T. S. Visible spectra of type II cytochrome P450-drug complexes: evidence that "incomplete" heme coordination is common. Drug Metab. Dispos. 2007, 35, 614-622.
11. Chiba, M.; Jin, L.; Neway, W.; Vacca, J. P.; Tata, J. R.; Chapman, K.; Lin, J. H. P450 interaction with HIV protease inhibitors: relationship between metabolic stability, inhibitory potency, and P450 binding spectra. Drug Metab. Dispos. 2001, 29, 1-3.
12. Roberts, A. G.; Campbell, A. P.; Atkins, W. M. The thermodynamic landscape of testosterone binding to cytochrome P 450 3A4: Ligand binding and spin state equilibria. Biochemistry 2005, 44, 1353-1366.
13. LeLean, J. E.; Moon, N.; Dunham, W. R.; Coon, M. J. EPR spectrometry of cytochrome P450 2B4: Effects of mutations and substrate binding. Biochem. Biophys. Res. Commun. 2000, 276, 762-766.
14. Tsai, R.; Yu, C. A.; Gunsalus, I. C.; Peisach, J.; Blumberg, W.; Orme-Johnson, W. H.; Beinert, H. Spin-state changes in cytochrome P-450cam on binding of specific substrates. Proc. Natl. Acad. Sci. U.S.A. 1970, 66, 1157-1163.
15. Chiba, M.; Tang, C.; Neway, W. E.; Williams, T. M.; Desolms, S. J.; Dinsmore, C. J.; Wai, J. S.; Lin, J. H. P450 interaction with farnesyl-protein transferase inhibitors. Metabolic stability, inhibitory potency, and P450 binding spectra in human liver microsomes. Biochem. Pharmacol. 2001, 62, 773-776.
16. Johnston, S. R.; Martin, L. A.; Head, J.; Smith, I.; Dowsett, M. Aromatase inhibitors: combinations with fulvestrant or signal transduction inhibitors as a strategy to overcome endocrine resistance. J. Steroid Biochem. Mol. Biol. 2005, 95, 173-181.
17. Denton, T. T.; Zhang, X.; Cashman, J. R. Nicotine-related alkaloids and metabolites as inhibitors of human cytochrome P-450 2A6. Biochem. Pharmacol. 2004, 67, 751-756.
18. Sellers, E. M.; Kaplan, H. L.; Tyndale, R. F. Inhibition of cytochrome P450 2A6 increases nicotine's oral bioavailability and decreases smoking. Clin. Pharmacol. Ther. 2000, 68, 35-43.
19. Ekins, S.; Mankowski, D. C.; Hoover, D. J.; Lawton, M. P.; Treadway, J. L.; Harwood, H. J., Jr. Three-dimensional quantitative structure-activity relationship analysis of human CYP51 inhibitors. Drug Metab. Dispos. 2007, 35, 493-500.
20. Gibbons, G. F. The role of cytochrome P450 in the regulation of cholesterol biosynthesis. Lipids 2002, 37, 1163-1170.
21. Zhang, W.; Ramamoorthy, Y.; Kilicarslan, T.; Nolte, H.; Tyndale, R. F.; Sellers, E. M. Inhibition of cytochromes P450 by antifungal imidazole derivatives. Drug Metab. Dispos. 2002, 30, 314-318.
22. Zarn, J. A.; Bruschweiler, B. J.; Schlatter, J. R. Azole fungicides affect mammalian steroidogenesis by inhibiting sterol 14 alpha-demethylase and aromatase. Environ. Health Perspect. 2003, 111, 255-261.
23. Evans, W. E.; Relling, M. V. Pharmacogenomics: translating functional genomics into rational therapeutics. Science 1999, 286, 487-491.
24. Rettie, A. E.; Jones, J. P. Clinical and toxicological relevance of Cyp2c9: Drug-drug interactions and pharmacogenetics. Annu. Rev. Pharmacol. Toxicol. 2005, 45, 477-494.
25. Rushmore, T. H.; Reider, P. J.; Slaughter, D.; Assang, C.; Shou, M. Bioreactor systems in drug metabolism: synthesis of cytochrome P450-generated metabolites. Metab. Eng. 2000, 2, 115-125.
26. BD Biosciences. 4′-Hydroxydiclofenac standard. BD Biosciences: San Jose, CA, 2005.
27. Shaw, P. M.; Hosea, N. A.; Thompson, D. V.; Lenius, J. M.; Guengerich, F. P. Reconstitution premixes for assays using purified recombinant human cytochrome P450, NADPH-cytochrome P450 reductase, and cytochrome b5. Arch. Biochem. Biophys. 1997, 348, 107-115.
28. Locuson, C. W.; Gannett, P. M.; Tracy, T. S. Heteroactivator effects on the coupling and spin state equilibrium of CYP2C9. Arch. Biochem. Biophys. 2006, 449, 115-129.
29. Jefcoate, C. R. Measurement of substrate and inhibitor binding to microsomal cytochrome P-450 by optical-difference spectroscopy. Methods Enzymol. 1978, 52.
30. Wester, M. R.; Yano, J. K.; Schoch, G. A.; Yang, C.; Griffin, K. J.; Stout, C. D.; Johnson, E. F. The structure of human cytochrome P4502C9 complexed with flurbiprofen at 2.0-angstrom resolution. J. Biol. Chem. 2004, 279, 35630-35637.
31. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A., Jr.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian 03, revision C.02; Gaussian, Inc.: Wallingford, CT, 2004.
32. Staroverov, V. N.; Scuseria, G. E.; Tao, J. M.; Perdew, J. P. Comparative assessment of a new nonempirical density functional: Molecules and hydrogen-bonded complexes. J. Chem. Phys. 2003, 119, 12129-12137.
33. Peterson, K. A.; Dolg, M. Unpublished results.
34. Woon, D. E.; Dunning, T. H. Gaussian-basis sets for use in correlated molecular calculations 0.3. The atoms aluminum through argon. J. Chem. Phys. 1993, 98, 1358-1371.
35. Kendall, R. A.; Dunning, T. H.; Harrison, R. J. Electron-affinities of the 1st-row atoms revisited-systematic basis-sets and wave-functions. J. Chem. Phys. 1992, 96, 6796-6806.
36. Dunning, T. H. Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen. J. Chem. Phys. 1989, 90, 1007-1023.
37. Cho, K. B.; Moreau, Y.; Kumar, D.; Rock, D. A.; Jones, J. P.; Shaik, S. Formation of the active species of cytochrome P450 by using iodosylbenzene: A case for spin-selective reactivity. Chem. - Eur. J. 2007, 13, 4103-4115.
38. Schenkman, J. B.; Sligar, S. G.; Cinti, D. L. Substrate interaction with cytochrome P-450. Pharmacol. Ther. 1981, 12, 43-71.
39. Dawson, J. H.; Andersson, L. A.; Sono, M. Spectroscopic investigations of ferric cytochrome P-450-CAM ligand complexes. Identification of the ligand trans to cysteinate in the native enzyme. J. Biol. Chem. 1982, 257, 3606-3617.
40. Verras, A.; Kuntz, I. D.; Ortiz de Montellano, P. R. Computer-assisted design of selective imidazole inhibitors for cytochrome p450 enzymes. J. Med. Chem. 2004, 47, 3572-3579.
41. Ahlstroem, M. M.; Zamora, I. Characterization of type II ligands in CYP2C9 and CYP3A4. J. Med. Chem. 2008, 51, 1755-1763.
42. Strickler, M.; Goldstein, B. M.; Maxfield, K.; Shireman, L.; Kim, G.; Matteson, D. S.; Jones, J. P. Crystallographic studies on the complex behavior of nicotine binding to P450cam (CYP101). Biochemistry 2003, 42, 11943-11950.
43. Podust, L. M.; Poulos, T. L.; Waterman, M. R. Crystal structure of cytochrome P450 14alpha-sterol demethylase (CYP51) from Mycobacterium tuberculosis in complex with azole inhibitors. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 3068-3073.
44. Cupp-Vickery, J. R.; Garcia, C.; Hofacre, A.; McGee-Estrada, K. Ketoconazole-induced conformational changes in the active site of cytochrome P450eryF. J. Mol. Biol. 2001, 311, 101-110.
45. Zhao, Y.; White, M. A.; Muralidhara, B. K.; Sun, L.; Halpert, J. R.; Stout, C. D. Structure of microsomal cytochrome P450 2B4 complexed with the antifungal drug bifonazole: iInsight into P450 conformational plasticity and membrane interaction. J. Biol. Chem. 2006, 281, 5973-5981.
46. Pellequer, J.-L.; Zhao, B.; Kao, H.-I.; Bell, C. W.; Li, K.; Li, Q. X.; Karu, A. E.; Roberts, V. A. Stabilization of bound polycyclic aromatic hydrocarbons by a p-cation interaction. J. Mol. Biol. 2000, 302, 691-699.
47. Dougherty, D. A.; Stauffer, D. A. Acetylcholine binding by a synthetic receptor: implications for biological recognition. Science (Washington, DC, U.S.) 1990, 250, 1558-1560.